sidier (version 3.0.1)

mutationSummary: Summary of observed mutations

Description

This function computes the number of substitutions and indels observed in a given alignment.

Usage

mutationSummary(align, addExtremes = FALSE, output = "brief")

Arguments

align

the name of the "DNAbin" alignment to be analysed. See "?read.dna" in the ape package for details about reading alignments.

addExtremes

a logical; if TRUE, additional nucleotide sites are included in both extremes of the alignment. This will allow estimating distances for alignments showing gaps in terminal positions.

output

a string; defines the kind of output. Two values are accepted: - "brief" (default) produces an output showing the number of mutations (sites and events). - "detailed" produces an output showing the number of mutations (sites and events), the position of each mutation, and the state of these sites per sequence (A, T, C, G or - for substitutions and 1 or 0 for indels).

Value

A list containing:

Sites

A matrix containing: the number of sites per sequence (Length); the number of constant and variable sites; the number of singletons and informative sites.

Events

A matrix containing: the number of substitution (singletons, informative, and total) and indel (singletons, informative, and total) events

Constants.Alignment

A matrix showing constant sites in the alignment (Only shown if output=="detailed").

Variables.Alignment

A matrix showing variable sites in the alignment (Only shown if output=="detailed").

Singletons.Alignment

A matrix showing singleton sites in the alignment (Only shown if output=="detailed").

Inforatives.Alignment

A matrix showing informative sites in the alignment (Only shown if output=="detailed").

Substitutions

A matrix showing substitution sites in the alignment (Only shown if output=="detailed").

Subst.Single

A matrix showing singleton substitution sites in the alignment (Only shown if output=="detailed").

Subst.Info

A matrix showing informative substitution sites in the alignment (Only shown if output=="detailed").

Gaps

A matrix showing gap sites in the alignment (Only shown if output=="detailed").

Gaps.Single

A matrix showing singleton gap sites in the alignment (Only shown if output=="detailed").

Gaps.Info

A matrix showing informative gap sites in the alignment (Only shown if output=="detailed").

Examples

cat(">Population1_sequence1",
"A-AGGGTC-CT---G",
">Population1_sequence2",
"TAA---TCGCT---G",
">Population1_sequence3",
"TAAGGGTCGCT---G",
">Population1_sequence4",
"TAA---TCGCT---G",
">Population2_sequence1",
"TTACGGTCG---TTG",
">Population2_sequence2",
"TAA---TCG---TTG",
">Population2_sequence3",
"TAA---TCGCTATTG",
">Population2_sequence4",
"TTACGGTCG---TTG",
">Population3_sequence1",
"TTA---TCG---TAG",
">Population3_sequence2",
"TTA---TCG---TAG",
">Population3_sequence3",
"TTA---TCG---TAG",
">Population3_sequence4",
"TTA---TCG---TAG",
     file = "ex3.fas", sep = "\n")

# Reading the alignment directly from file and saving no output file:
library(ape)
mutationSummary (align=read.dna("ex3.fas",format="fasta"))
mutationSummary (align=read.dna("ex3.fas",format="fasta"),output="detailed")

#A more complex alignment
data(ex_alignment1) # this will read a fasta file with the name 'alignExample'
mutationSummary(align=alignExample,addExtremes=TRUE)